R News

CHANGES IN R VERSION 2.12.0

NEW FEATURES

Reading a packages's ‘CITATION’ file now defaults to
ASCII rather than Latin-1: a package with a non-ASCII
‘CITATION’ file should declare an encoding in its
‘DESCRIPTION’ file and use that encoding for the
‘CITATION’ file.

difftime() now defaults to the "tzone"
attribute of "POSIXlt" objects rather than to the current
timezone as set by the default for the tz argument. (Wish
of PR#14182.)

pretty() is now generic, with new methods for
"Date" and "POSIXt" classes (based on code
contributed by Felix Andrews).

unique() and match() are now faster on
character vectors where all elements are in the global CHARSXP
cache and have unmarked encoding (ASCII). Thanks to Matthew
Dowle for suggesting improvements to the way the hash code is
generated in ‘unique.c’.

The enquote() utility, in use internally, is exported now.

.C() and .Fortran() now map non-zero return
values (other than NA_LOGICAL) for logical vectors to
TRUE: it has been an implicit assumption that they are
treated as true.

The print() methods for "glm" and "lm"
objects now insert linebreaks in long calls in the same way that
the print() methods for "summary.[g]lm" objects
have long done. This does change the layout of the examples for
a number of packages, e.g. MASS. (PR#14250)

It gains an argument hessian to be passed to
optim(), which allows all the ... arguments to be
intended for f() and grad(). (PR#14071)

curve() now allows expr to be an object of
mode "expression" as well as "call" and
"function".

The "POSIX[cl]t" methods for Axis() have been
replaced by a single method for "POSIXt".

There are no longer separate plot() methods for
"POSIX[cl]t" and "Date": the default method has
been able to handle those classes for a long time. This
inter alia allows a single date-time object to be
supplied, the wish of PR#14016.

The methods had a different default ("") for xlab.

Classes "POSIXct", "POSIXlt" and
"difftime" have generators .POSIXct(),
.POSIXlt() and .difftime(). Package authors are
advised to make use of them (they are available from R 2.11.0) to
proof against planned future changes to the classes.

The ordering of the classes has been changed, so "POSIXt"
is now the second class. See the document ‘Updating
packages for changes in R 2.12.x’ on
http://developer.r-project.org for the consequences for a
handful of CRAN packages.

The "POSIXct" method of as.Date() allows a
timezone to be specified (but still defaults to UTC).

New list2env() utility function as an inverse of
as.list(<environment>) and for fast multi-assign()
to existing environment. as.environment() is now generic
and uses list2env() as list method.

There are several small changes to output which ‘zap’
small numbers, e.g. in printing quantiles of residuals in
summaries from "lm" and "glm" fits, and in test
statisics in print.anova().

Special names such as "dim", "names", etc, are
now allowed as slot names of S4 classes, with "class" the
only remaining exception.

File ‘.Renviron’ can have architecture-specific versions
such as ‘.Renviron.i386’ on systems with sub-architectures.

installed.packages() has a new argument
subarch to filter on sub-architecture.

The summary() method for packageStatus() now
has a separate print() method.

The default summary() method returns an object
inheriting from class "summaryDefault" which has a
separate print() method that calls zapsmall() for
numeric/complex values.

The startup message now includes the platform and if used,
sub-architecture: this is useful where different
(sub-)architectures run on the same OS.

The getGraphicsEvent() mechanism now allows multiple windows
to return graphics events, through the new functions
setGraphicsEventHandlers(), setGraphicsEventEnv(), and
getGraphicsEventEnv(). (Currently implemented in the
windows() and X11() devices.)

tools::texi2dvi() gains an index argument,
mainly for use by R CMD Rd2pdf.

It avoids the use of texindy by texinfo's
texi2dvi >= 1.157, since that does not emulate
'makeindex' well enough to avoid problems with special characters
(such as (, {, !) in indices.

The ability of readLines() and scan() to
re-encode inputs to marked UTF-8 strings on Windows since R 2.7.0
is extended to non-UTF-8 locales on other OSes.

Sys.chmod() allows argument mode to be a
vector, recycled along paths.

There are |, & and xor() methods for
classes "octmode" and "hexmode", which work
bitwise.

Environment variables R_DVIPSCMD, R_LATEXCMD,
R_MAKEINDEXCMD, R_PDFLATEXCMD are no longer used
nor set in an R session. (With the move to
tools::texi2dvi(), the conventional environment variables
LATEX, MAKEINDEX and PDFLATEX will be used.
options("dvipscmd") defaults to the value of DVIPS,
then to "dvips".)

New function isatty() to see if terminal connections are
redirected.

summaryRprof() returns the sampling interval in
component sample.interval and only returns in
by.self data for functions with non-zero self times.

print(x) and str(x) now indicate if an empty
list x is named.

install.packages() and remove.packages() with
lib unspecified and multiple libraries in
.libPaths() inform the user of the library location used
with a message rather than a warning.

There is limited support for multiple compressed streams on a
file: all of [bgx]zfile() allow streams to be appended to an
existing file, but bzfile() reads only the first stream.

Function person() in package utils now uses
a given/family scheme in preference to first/middle/last, is
vectorized to handle an arbitrary number of persons, and gains a
role argument to specify person roles using a controlled
vocabulary (the MARC relator terms).

Added support for subsetting "raster" objects, plus
assigning to a subset, conversion to a matrix (of colour
strings), and comparisons (== and !=).

Added a new parseLatex() function (and related
functions deparseLatex() and latexToUtf8()) to
support conversion of bibliographic entries for display in R.

Text rendering of \itemize in help uses a Unicode
bullet in UTF-8 and most single-byte Windows locales.

Added support for polygons with holes to the graphics
engine. This is implemented for the pdf(),
postscript(), x11(type="cairo"), windows(),
and quartz() devices (and associated raster formats),
but not for x11(type="Xlib") or xfig() or
pictex(). The user-level interface is the
polypath() function in graphics and
grid.path() in grid.

File ‘NEWS’ is now generated at installation with a
slightly different format: it will be in UTF-8 on platforms using
UTF-8, and otherwise in ASCII. There is also a PDF version,
‘NEWS.pdf’, installed at the top-level of the R distribution.

kmeans(x, 1) now works. Further, kmeans now
returns between and total sum of squares.

arrayInd() and which() gain an argument
useNames. For arrayInd, the default is now false,
for speed reasons.

As is done for closures, the default print method for
the formula class now displays the associated environment if it is
not the global environment.

A new facility has been added for inserting code into a
package without re-installing it, to facilitate testing
changes which can be selectively added and backed out. See
?insertSource.

New function readRenviron to (re-)read files in the
format of ‘~/.Renviron’ and ‘Renviron.site’.

require() will now return FALSE (and not fail)
if loading the package or one of its dependencies fails.

aperm() now allows argument perm to be a
character vector when the array has named dimnames (as the results
of table() calls do). Similarly, array() allows
MARGIN to be a character vector. (Based on suggestions of
Michael Lachmann.)

Package utils now exports and documents functions
aspell_package_Rd_files() and
aspell_package_vignettes() for spell checking package Rd
files and vignettes using Aspell, Ispell or Hunspell.

Package news can now be given in Rd format, and
news() prefers these ‘inst/NEWS.Rd’ files to old-style
plain text ‘NEWS’ or ‘inst/NEWS’ files.

New simple function packageVersion().

The PCRE library has been updated to version 8.10.

The standard Unix-alike terminal interface declares its name
to readline as 'R', so that can be used for conditional sections
in ‘~/.inputrc’ files.

‘Writing R Extensions’ now stresses that the standard
sections in ‘.Rd’ files (other than \alias,
\keyword and \note) are intended to be unique, and
the conversion tools now drop duplicates with a warning.

The ‘.Rd’ conversion tools also warn about an unrecognized type
in a \docType section.

ecdf() objects now have a quantile() method.

format() methods for date-time objects now attempt to make
use of a "tzone" attribute with "%Z" and
"%z" formats, but it is not always possible. (Wish of
PR#14358.)

tools::texi2dvi(file, clean = TRUE) now works in more
cases (e.g. where emulation is used and when ‘file’ is not in
the current directory).

New function droplevels() to remove unused factor levels.

system(command, intern = TRUE) now gives an error on
a Unix-alike (as well as on Windows) if command cannot be
run. It reports a non-success exit status from running
command as a warning.

On a Unix-alike an attempt is made to return the actual exit
status of the command in system(intern = FALSE): previously
this had been system-dependent but on POSIX-compliant systems the
value return was 256 times the status.

system() has a new argument ignore.stdout
which can be used to (portably) ignore standard output.

system(intern = TRUE) and pipe() connections
are guaranteed to be avaliable on all builds of R.

Sys.which() has been altered to return "" if
the command is not found (even on Solaris).

A facility for defining reference-based S4 classes (in the
OOP style of Java, C++, etc.) has been added experimentally to
package methods; see ?ReferenceClasses.

The predict method for "loess" fits gains an
na.action argument which defaults to na.pass rather
than the previous default of na.omit.

Predictions from "loess" fits are now named from the row
names of newdata.

Parsing errors detected during Sweave() processing
will now be reported referencing their original location in the
source file.

An experimental new programming model has been added to
package methods for reference (OOP-style) classes and
methods. See ?ReferenceClasses.

bzip2 has been updated to version 1.0.6 (bug-fix release).
--with-system-bzlib now requires at least version 1.0.6.

R now provides ‘jss.cls’ and ‘jss.bst’ (the class
and bib style file for the Journal of Statistical Software) as
well as ‘RJournal.bib’ and ‘Rnews.bib’, and
R CMD ensures that the ‘.bst’ and ‘.bib’ files
are found by BibTeX.

Functions using the TAR environment variable no longer
quote the value when making system calls. This allows
values such as tar --force-local, but does require
additional quotes in, e.g., TAR = "'/path with spaces/mytar'".

DEPRECATED & DEFUNCT

Supplying the parser with a character string containing both
octal/hex and Unicode escapes is now an error.

The save argument of require() now defaults to
FALSE and save = TRUE is now deprecated. (This
facility is very rarely actually used, and was superseded by the
Depends field of the ‘DESCRIPTION’ file long ago.)

R CMD check --no-latex is deprecated in favour of
--no-manual.

R CMD Sd2Rd is formally deprecated and will be
removed in R 2.13.0.

PACKAGE INSTALLATION

install.packages() has a new argument
libs_only to optionally pass --libs-only to
R CMD INSTALL and works analogously for Windows binary
installs (to add support for 64- or 32-bit Windows).

When sub-architectures are in use, the installed
architectures are recorded in the Archs field of the
‘DESCRIPTION’ file. There is a new default filter,
"subarch", in available.packages() to make use of
this.

Code is compiled in a copy of the ‘src’ directory when a
package is installed for more than one sub-architecture: this
avoid problems with cleaning the sources between building
sub-architectures.

R CMD INSTALL --libs-only no longer overrides the
setting of locking, so a previous version of the package will be
restored unless --no-lock is specified.

UTILITIES

R CMD Rprof|build|check are now based on R rather
than Perl scripts. The only remaining Perl scripts are the
deprecated R CMD Sd2Rd and install-info.pl (used
only if install-info is not found) as well as some
maintainer-mode-only scripts.

NB: because these have been completely rewritten, users
should not expect undocumented details of previous
implementations to have been duplicated.

R CMD check has a new argument --extra-arch
to confine tests to those needed to check an additional
sub-architecture.

Its check for “Subdirectory 'inst' contains no files” is
more thorough: it looks for files, and warns if there are only
empty directories.

Environment variables such as R_LIBS and those used for
customization can be set for the duration of checking via a file
‘~/.R/check.Renviron’ (in the format used by
‘.Renviron’, and with sub-architecture specific versions
such as ‘~/.R/check.Renviron.i386’ taking precedence).

There are new options --multiarch to check the package
under all of the installed sub-architectures and
--no-multiarch to confine checking to the
sub-architecture under which check is invoked. If
neither option is supplied, a test is done of installed
sub-architectures and all those which can be run on the current
OS are used.

Unless multiple sub-architectures are selected, the install done
by check for testing purposes is only of the current
sub-architecture (viaR CMD INSTALL --no-multiarch).

It will skip the check for non-ascii characters in code or data
if the environment variables _R_CHECK_ASCII_CODE_ or
_R_CHECK_ASCII_DATA_ are respectively set to FALSE.
(Suggestion of Vince Carey.)

R CMD Rd2dvi makes use of tools::texi2dvi()
to process the package manual. It is now implemented entirely in
R (rather than partially as a shell script).

R CMD Rprof now uses utils::summaryRprof()
rather than Perl. It has new arguments to select one of the
tables and to limit the number of entries printed.

R CMD Sweave now runs R with --vanilla so
the environment setting of R_LIBS will always be used.

C-LEVEL FACILITIES

lang5() and lang6() (in addition to
pre-existing lang[1-4]()) convenience functions for easier
construction of eval() calls. If you have your own
definition, do wrap it inside #ifndef lang5 .... #endif
to keep it working with old and new R.

Header ‘R.h’ now includes only the C headers it itself needs,
hence no longer includes errno.h. (This helps avoid problems
when it is included from C++ source files.)

Headers ‘Rinternals.h’ and ‘R_ext/Print.h’ include
the C++ versions of ‘stdio.h’ and ‘stdarg.h’
respectively if included from a C++ source file.

INSTALLATION

A C99 compiler is now required, and more C99 language features
will be used in the R sources.

Tcl/Tk >= 8.4 is now required (increased from 8.3).

System functions access, chdir and
getcwd are now essential to configure R. (In practice
they have been required for some time.)

make check compares the output of the examples
from several of the base packages to reference output rather than
the previous output (if any). Expect some differences due to
differences in floating-point computations between platforms.

File ‘NEWS’ is no longer in the sources, but generated as
part of the installation. The primary source for changes is now
‘doc/NEWS.Rd’.

The popen system call is now required to build R.
This ensures the availability of system(intern = TRUE),
pipe() connections and printing from postscript().

The pkg-config file ‘libR.pc’ now also works
when R is installed using a sub-architecture.

R has always required a BLAS that conforms to IE60559
arithmetic, but after discovery of more real-world problems caused
by a BLAS that did not, this is tested more thoroughly in this
version.

BUG FIXES

Calls to selectMethod() by default no longer cache
inherited methods. This could previously corrupt methods used by
as().

The densities of non-central chi-squared are now more accurate
in some cases in the extreme tails, e.g. dchisq(2000, 2,
1000), as a series expansion was truncated too early.
(PR#14105)

pt() is more accurate in the left tail for ncp
large, e.g. pt(-1000, 3, 200). (PR#14069)

The default C function (R_binary) for binary ops now
sets the S4 bit in the result if either argument is an S4 object.
(PR#13209)

source(echo=TRUE) failed to echo comments that
followed the last statement in a file.

S4 classes that contained one of "matrix",
"array" or "ts" and also another class now accept
superclass objects in new(). Also fixes failure to call
validObject() for these classes.

Conditional inheritance defined by argument test in
methods::setIs() will no longer be used in S4 method
selection (caching these methods could give incorrect results).
See ?setIs.

The signature of an implicit generic is now used by
setGeneric() when that does not use a definition nor
explicitly set a signature.

A bug in callNextMethod() for some examples with
"..." in the arguments has been fixed. See file
‘src/library/methods/tests/nextWithDots.R’ in the sources.

The abs.tol control parameter to nlminb()
now defaults to 0.0 to avoid false declarations of
convergence in objective functions that may go negative.

The standard Unix-alike termination dialog to ask whether to
save the workspace takes a EOF response as n to avoid
problems with a damaged terminal connection. (PR#14332)

Added warn.unused argument to hist.default()
to allow suppression of spurious warnings about graphical
parameters used with plot=FALSE. (PR#14341)

predict.lm(), summary.lm(), and indeed
lm() itself had issues with residual DF in zero-weighted
cases (the latter two only in connection with empty
models). (Thanks to Bill Dunlap for spotting the
predict() case.)

aperm() treated resize = NA as resize =
TRUE.

constrOptim() now has an improved convergence
criterion, notably for cases where the minimum was (very close to)
zero; further, other tweaks inspired from code proposals by Ravi
Varadhan.

Rendering of S3 and S4 methods in man pages has been
corrected and made consistent across output formats.

Simple markup is now allowed in \title sections
in ‘.Rd’ files.

The behaviour of as.logical() on factors (to use the
levels) was lost in R 2.6.0 and has been restored.

prompt() did not backquote some default arguments in
the \usage section. (Reported by Claudia Beleites.)

writeBin() disallows attempts to write 2GB or
more in a single call. (PR#14362)

new() and getClass() will now work if Class
is a subclass of "classRepresentation" and should also be
faster in typical calls.

The summary() method for data frames makes a better
job of names containing characters invalid in the current locale.

[[ sub-assignment for factors could create an invalid
factor (reported by Bill Dunlap).

Negate(f) would not evaluate argument f
until first use of returned function (reported by Olaf Mersmann).

quietly=FALSE is now also an optional argument of
library(), and consequently, quietly is now
propagated also for loading dependent packages, e.g., in
require(*, quietly=TRUE).

If the loop variable in a for loop was deleted, it
would be recreated as a global variable. (Reported by Radford
Neal; the fix includes his optimizations as well.)

Task callbacks could report the wrong expression when
the task involved parsing new code. (PR#14368)

getNamespaceVersion() failed; this was an
accidental change in 2.11.0. (PR#14374)

identical() returned FALSE for external
pointer objects even when the pointer addresses were the same.

L$a@x[] <- val did not duplicate in a case it should have.

tempfile() now always gives a random file name (even
if the directory is specified) when called directly after
startup and before the R RNG had been used. (PR#14381)

backSpline(.) behaved incorrectly when the knot
sequence was decreasing. (PR#14386)

The reference BLAS included in R was assuming that
0*x and x*0 were always zero (whereas they could be
NA or NaN in IEC 60559 arithmetic). This was seen
in results from tcrossprod, and for example that
log(0) %*% 0 gave 0.

The calculation of whether text was completely outside
the device region (in which case, you draw nothing)
was wrong for screen devices (which have [0, 0] at top-left).
The symptom was (long) text disappearing when
resizing a screen window (to make it smaller). (PR#14391)

model.frame(drop.unused.levels = TRUE) did not
take into account NA values of factors when deciding to
drop levels. (PR#14393)

Both library() and loadNamespace() now record
absolute paths for use by searchpaths() and
getNamespaceInfo(ns, "path").

The self-starting model NLSstClosestX failed if some
deviation was exactly zero. (PR#14384)

X11(type = "cairo") (and other devices such as
png using cairographics) and which use Pango font selection
now work around a bug in Pango when very small fonts (those with
sizes between 0 and 1 in Pango's internal units) are requested.
(PR#14369)

Added workaround for the font problem with X11(type =
"cairo") and similar on Mac OS X whereby italic and bold styles
were interchanged. (PR#13463 amongst many other reports.)

source(chdir = TRUE) failed to reset the working
directory if it could not be determined – that is now an error.

Fix for crash of example(rasterImage) on
x11(type="Xlib").

Force Quartz to bring the on-screen display up-to-date
immediately before the snapshot is taken by grid.cap()
in the Cocoa implementation. (PR#14260)

Subassignment by [, [[ or $ on an
expression object with value NULL coerced the object to a
list.

CHANGES IN R VERSION 2.11.1 patched

NEW FEATURES

install.packages() has a new optional argument
INSTALL_opts which can be used to pass options to
R CMD INSTALL for source-package installs.

R CMD check now runs the package-specific tests
with LANGUAGE=en to facilitate comparison to
‘.Rout.save’ files.

sessionInfo() gives more detailed platform
information, including 32/64-bit and the sub-architecture if one
is used.

DEPRECATED & DEFUNCT

The use of Perl configuration variables for R CMD
check (as previously documented in ‘Writing R
Extensions’) is deprecated and will be removed in R 2.12.0. Use
the environment variables documented in ‘R Internals’
instead.

BUG FIXES

R CMD Rd2dvi failed if run from a path containing
space(s). This also affected R CMD check, which calls
Rd2dvi.

Text help rendering of \tabular{} has been
improved: under some circumstances leading blank columns were
not rendered.

strsplit(x, fixed=TRUE) marked UTF-8 strings with the
local encoding when no splits were found.

weighted.mean(NA, na.rm=TRUE) and similar now returns
NaN again, as it did prior to R 2.10.0.

R CMD had a typo in its detection of whether the
environment variable TEXINPUTS was set (reported by Martin
Morgan).

The command-line parser could mistake
--file=size... for one of the options for setting limits
for Ncells or Vcells.

The internal strptime() could corrupt its copy of the
timezone which would then lead to spurious warnings. (PR#14338)

dir.create(recursive = TRUE) could fail if one of the
components existed but was a directory on a read-only file system.
(Seen on Solaris, where the error code returned is not even listed
as possible on the man page.)

The postscript() and pdf() devices will now
allow lwd values less than 1 (they used to force such
values to be 1).

approxfun(), approx(), splinefun()
and spline() could be confused by x values that
were different but so close as to print identically.
(PR#14377)

CHANGES IN R VERSION 2.11.1

NEW FEATURES

R CMD INSTALL checks if dependent packages are
available early on in the installation of source packages,
thereby giving clearer error messages.

R CMD INSTALL --build now names the file in the
format used for Mac OS X binary files on that platform.

BIC() in package stats4 now also works with
multiple fitted models, analogously to AIC().

DEPRECATED & DEFUNCT

Use of file extension ‘.C’ for C++ code in packages is now
deprecated: it has caused problems for some makes on
case-insensitive file systems (although it currently works
with the recommended toolkits).

INSTALLATION

Command gnutar is preferred to tar
when configure sets TAR. This is needed on Mac OS 10.6,
where the default tar, bsdtar 2.6.2, has been
reported to produce archives with illegal extensions to tar
(according to the POSIX standard).

BUG FIXES

The C function mkCharLenCE now no longer reads past
len bytes (unlikely to be a problem except in user
code). (PR#14246)

On systems without any default LD_LIBRARY_PATH (not
even ‘/usr/local/lib’), [DY]LIB_LIBRARY_PATH is now
set without a trailing colon. (PR#13637)

More efficient implementation of utf8ToInt() on long
multi-byte strings with many multi-byte characters. (PR#14262)

aggregate.ts() gave platform-dependent results due to
rounding error for ndeltat != 1.

package.skeleton() sometimes failed to fix filenames
for ‘.R’ or ‘.Rd’ files to start with an alphanumeric.
(PR#14253)

It also failed when only an S4 class without any methods was
defined. (PR#14280)

CHANGES IN R VERSION 2.11.0

SIGNIFICANT USER-VISIBLE CHANGES

Packages must have been installed under R >= 2.10.0, as the
current help system is the only one now supported.

A port to 64-bit Windows is now available as well as binary
package repositiories: see the ‘R Administration and
Installation Manual’.

Argument matching for primitive functions is now done in the
same way as for interpreted functions except for the deliberate
exceptions

call switch .C .Fortran .Call .External

all of which use positional matching for their first argument,
and also some internal-use-only primitives.

The default device for command-line R at the console on Mac OS X
is now quartz() and not X11().

NEW FEATURES

The open modes for connections are now interpreted
more consistently. open = "r" is now equivalent to
open = "rt" for all connections. The default open =
"" now means "rt" for all connections except the
compressed-file connections gzfile(), bzfile() and
xzfile() for which it means "rb".

R CMD INSTALL now uses the internal untar()
function in package utils: this ensures that all platforms
can install bzip2- and xz-compressed
tarballs. In case this causes problems (as it has on some
Windows file systems when run from Cygwin tools) it can be
overridden by the environment variable R_INSTALL_TAR:
setting this to a modern external tar program will speed up
unpacking of large (tens of Mb or more) tarballs.

help(try.all.packages = TRUE) is much faster
(although the time taken by the OS to find all the packages the
first time it is used can dominate the time).

R CMD check has a new option --timings
to record per-example timings in file
‘<pkg>.Rcheck/<pkg>-Ex.timings’.

The TRE library has been updated to version 0.8.0 (minor bugfixes).

grep[l], [g]sub and [g]regexpr now work
in bytes in an 8-bit locales if there is no marked UTF-8 input
string: this will be somewhat faster, and for [g]sub()
give the result in the native encoding rather than in UTF-8
(which returns to the behaviour prior to R 2.10.0).

A new argument skipCalls has been added to
browser() so that it can report the original context when
called by other debugging functions.

More validity checking of UTF-8 and MBCS strings is done by
agrep() and the regular-expression matching functions.

The undocumented restriction on gregexpr() to
length(text) > 0 has been removed.

Package tcltk now sends strings to Tcl in UTF-8: this
means that strings with a marked UTF-8 encoding are supported in
non-UTF-8 locales.

The graphics engine now supports rendering of raster (bitmap)
images, though not all graphics devices can provide (full)
support. Packages providing graphics devices (e.g., Cairo,
RSvgDevice, cairoDevice) will need to be reinstalled.

There is also support in the graphics engine for capturing
raster images from graphics devices (again not supported
on all graphics devices).

R CMD check now also checks if the package and
namespace can be unloaded: this provides a check of the
.Last.lib() and .onUnload() hook functions (unless
--install=fake).

prop.table(x) now accepts a one-dimensional table for
x.

A new function vapply() has been added, based on a
suggestion from Bill Dunlap. It requires that a template for the
function value be specified, and uses it to determine the output
type and to check for consistency in the function values.

The main HTML help page now links to a reformatted copy of
this ‘NEWS’ file. (Suggested by Henrik Bengtsson.) Package
index files link to the package ‘DESCRIPTION’ and
‘NEWS’ files and a list of demos when using dynamic help.

The [ method for class "AsIs" allows the next
method to change the underlying class. (Wish of Jens
Oehlschlägel.)

write.csv[2] no longer allow argument append
to be changed: as ever, direct calls to write.table() give
more flexibility as well as more room for error.

The index page for HTML help for a package now collapses
multiple signatures for S4 methods into a single entry.

The use of .required by require() and
detach() has been replaced by .Depends which is set
from the Depends field of a package (even in packages with
name spaces). By default detach() prevents such
dependencies from being detached: this can be overridden by the
argument force.

bquote() has been extended to work on function
definitions. (Wish of
PR#14031).

detach() when applied to an object other than a
package returns the environment that has been detached, to
parallel attach().

readline() in non-interactive use returns ""
and does not attempt to read from the ‘terminal’.

New function file_ext() in package tools.

xtfrm() is now primitive and internally generic, as
this allows S4 methods to be set on it without name-space scoping
issues.

There are now "AsIs" and "difftime" methods, and
the default method uses unclass(x) if is.numeric(x)
is true (which will be faster but relies on is.numeric()
having been set correctly for the class).

is.numeric(x) is now false for a "difftime"
object (multiplication and division make no sense for such
objects).

The default method of weighted.mean(x, w) coerces
w to be numeric (aka double); previously only integer
weights were coerced. Zero weights are handled specially so an
infinite value with zero weight does not force an NaN
result.

There is now a "difftime" method.

bug.report() now has arguments package and
lib.loc to generate bug reports about packages. When
this is used, it looks for a BugReports field in the
package ‘DESCRIPTION’ file, which will be assumed to be a
URL at which to submit the report, and otherwise generates an
email to the package maintainer. (Suggested by Barry
Rowlingson.)

quantile() now has a method for the date-time class
"POSIXt", and types 1 and 3 (which never interpolate) work
for Dates and ordered factors.

length(<POSIXlt>) now returns the length of the
corresponding abstract timedate-vector rather than always 9 (the
length of the underlying list structure). (Wish of PR#14073
and PR#10507.)

select.list() gains a graphics argument to
allow Windows/Mac users to choose the text interface. This
changes the behaviour of new.packages(ask=TRUE) to be like
update.packages(ask=TRUE) on those platforms in using a
text menu: use ask="graphics" for a graphical menu.

New function chooseBioCmirror() to set the
"BioC_mirror" option.

The R grammar now prevents using the argument name
in signatures of S4 methods for $ and $<-, since
they will always be called with a character string value for
name. The implicit S4 generic functions have been
changed to reflect this: packages which included name in
the signature of their methods need to be updated and
re-installed.

The handling of the method argument of glm()
has been refined following suggestions by Ioannis Kosmidis and
Heather Turner.

str() gains a new argument list.len with
default 99, limiting the number of list() items (per
level), thanks to suggestions from David Winsenius.

Having formal arguments of an S4 method in a different order
from the generic is now an error (the warning having been
ignored by some package maintainers for a long time).

New functions enc2native() and enc2utf8()
convert character vectors with possibly marked encodings to the
current locale and UTF-8 respectively.

Unrecognized escapes and embedded nuls in character strings are
now an error, not just a warning. Thus option "warnEscapes"
is no longer needed. rawToChar() now removes trailing nuls
silently, but other embedded nuls become errors.

Informational messages about masked objects displayed when a
package is attached are now more compact, using strwrap()
instead of one object per line.

print.rle() gains argument prefix.

download.file() gains a "curl" method, mainly
for use on platforms which have curl but not
wget, but also for some hard-to-access URLs.

file() has a new argument raw which may help
if it is used with something other than a regular file, e.g. a
character device.

New function strtoi(), a wrapper for the C function
strtol.

as.octmode() and as.hexmode() now allow inputs
of length other than one.

The format() and print() methods for
"octmode" now preserve names and dimensions (as those for
"hexmode" did).

The format() methods for classes "octmode" and
"hexmode" gain a width argument.

seq.int() returns an integer result in some further cases
where seq() does, e.g. seq.int(1L, 9L, by = 2L).

Added \subsection{}{} macro to Rd syntax, for
subsections within sections.

n-dimensional arrays with dimension names can now be indexed
by an n-column character matrix. The indices are matched against
the dimension names. NA indices are propagated to the
result. Unmatched values and "" are not allowed and
result in an error.

The ‘fuzz’ used by seq() and seq.int() has
been reduced from 1e-7 to 1e-10, which should be
ample for the double-precision calculations used in R. It
ensures that the fuzz never comes into play with sequences of
integers (wish of PR#14169).

The default value of RSiteSearch(restrict=) has been
changed to include vignettes but to exclude R-help. The R-help
archives available have been split, with a new option of
"Rhelp10" for those from 2010.

New function rasterImage() in the graphics
package for drawing raster images.

stats:::extractAIC.coxph() now omits aliased terms
when computing the degrees of freedom (suggestion of Terry
Therneau).

cor() and cov() now test for misuse with
non-numeric arguments, such as the non-bug report PR#14207.

pchisq(ncp =, log.p = TRUE) is more accurate for
probabilities near one. E.g. pchisq(80, 4, ncp=1,
log.p=TRUE). (Maybe what was meant in PR#14216.)

maintainer() has been added, to give convenient
access to the name of the maintainer of a package (contributed by
David Scott).

sample() and sample.int() allow zero items to
be sampled from a zero-length input. sample.int() gains a
default value size=n to be more similar to
sample().

switch() returned NULL on error (not
previously documented on the help page): it now does so
invisibly, analogously to if-without-else.

It is now primitive: this means that argument EXPR is
always matched to the first argument and there is no danger of
partial matching to later named arguments.

Primitive functions UseMethod(), attr(),
attr<-(), on.exit(), retracemem() and
substitute() now use standard argument matching (rather
than positional matching). This means that all multi-argument
primitives which are not internal now use standard argument
matching except where positional matching is desirable (as for
switch(), call(), .C() ...).

All the one-argument primitives now check that any name
supplied for their first argument is a partial match to the
argument name as documented on the help page: this also
applies to replacement functions of two arguments.

base::which() uses a new .Internal function
when arr.ind is FALSE resulting in a 10x speedup.
Thanks to Patrick Aboyoun for implementation suggestions.

Help conversion to text now uses the first part of
\enc{}{} markup if it is representable in the current
output encoding. On the other hand, conversion to LaTeX with the
default outputEncoding = "ASCII" uses the second part.

A new class "listOfMethods" has been introduced to
represent the methods in a methods table, to replace the
deprecated class "MethodsList".

any() and all() return early if possible.
This may speed up operations on long vectors.

strptime() now accepts "%z" (for the offset
from UTC in the RFC822 format of +/-hhmm).

The PCRE library has been updated to version 8.02, a bug-fix
release which also updates tables to Unicode 5.02.

Functions which may use a graphical select.list()
(including menu() and install.packages()) now check
on a Unix-alike that Tk can be started (and not just
capabilities("tcltk") && capabilities("X11")).

The parser no longer marks strings containing octal or hex
escapes as being in UTF-8 when entered in a UTF-8 locale.

On platforms with cairo but not Pango (notably Mac OS X) the
initial default X11() type is set to "Xlib": this avoids
several problems with font selection when done by cairo rather
than Pango (at least on Mac OS X).

New function arrayInd() such that which(x,
arr.ind = TRUE) for an array 'x' is now equivalent to
arrayInd(which(x), dim(x), dimnames(x)).

DEPRECATED & DEFUNCT

Bundles of packages are defunct.

stats::clearNames() is defunct: use unname().

Basic regular expressions are defunct, and
strsplit(), grep(), grepl(), sub(),
gsub(), regexpr() and gregexpr() no longer
have an extended argument.

methods::trySilent() is defunct.

index.search() (which was deprecated in 2.10.0) is no
longer exported and has a different argument list.

Use of multiple arguments to return() is now defunct.

The use of UseMethod() with more than two arguments
is now defunct.

In the methods package, the "MethodsList"
metadata objects which had been superseded by hash tables
(environments) since R 2.8.0 are being phased out. Objects of
this class are no longer assigned or used as metadata by the
package.

getMethods() is now deprecated, with its internal use replaced
by findMethods() and other changes. Creating objects from the
"MethodsList" class is also deprecated.

Parsing strings containing both octal/hex and Unicode escapes
now gives a warning and will become an error in R 2.12.0.

INSTALLATION

UTF-8 is now used for the reference manual and package
manuals. This requires LaTeX ‘2005/12/01’ or later.

configure looks for a POSIX compliant
tr, Solaris's /usr/ucb/tr having been found
to cause Rdiff to malfunction.

configure is now generated with autoconf
2.65, which works better on recent systems and on Mac OS X.

PACKAGE INSTALLATION

Characters in R source which are not translatable to the
current locale are now handled more tolerantly: these will be
converted to hex codes with a warning. Such characters are
only really portable if they appear in comments.

R CMD INSTALL now tests that the installed package
can be loaded (and backs out the installation if it cannot): this
can be suppressed by --no-test-load. This avoids
installing/updating a package that cannot be used: common causes
of failures to load are missing/incompatible external software
and missing/broken dependent packages.

Package installation on Windows for a package with a
‘src’ directory now checks if a DLL is created unless there
is a ‘src/Makefile.win’ file: this helps catch broken
installations where the toolchain has not reported problems in
building the DLL. (Note: this can be any DLL, not just one named
‘<pkg-name>.dll’.)

BUG FIXES

Using with(), eval() etc with a list with some
unnamed elements now works.
(PR#14035)

The "quick" dispatch of S4 methods for primitive
functions was not happening, forcing a search each time.
(Dispatch for closures was not affected.) A side effect is that
default values for arguments in a method that do not have
defaults in the generic will now be ignored.

Trying to dispatch S4 methods for primitives during the search
for inherited methods slows that search down and potentially
could cause an infinite recursion. An internal switch was
added to turn off all such methods from
findInheritedMethods().

R framework installation (on Mac OS X) would not work
properly if a rogue Resources directory was present at the
top level. Such a non-symlink will now be renamed to
Resources.old (and anything previously named
Resources.old removed) as part of the framework
installation process.

The checks for conforming S4 method arguments could fail
when the signature of the generic function omitted some of the
formal arguments (in addition to ...). Arguments omitted
from the method definition but conforming (per the documentation)
should now be ignored (treated as "ANY") in dispatching.

The computations for S4 method evaluation when ...
was in the signature could fail, treating ... as an
ordinary symbol. This has been fixed, for the known cases.

fisher.test() no longer gives a P-value very
slightly > 1, in some borderline cases.

Internal function matchArgs() no longer modifies the
general purpose bits of the SEXPs that make up the formals
list of R functions. This fixes an invalid error message that
would occur when a garbage collection triggered a second call to
matchArgs for the same function via a finalizer.

gsub() in 2.10.x could fail from stack overflow for
extremely long strings due to temporary data being allocated on
the stack. Also, gsub() with fixed=TRUE is in some
circumstances considerably faster.

Several primitives, including attributes(),
attr<-()interactive(), nargs() and
proc.time(), did not check that they were called with the
correct number of arguments.

A potential race condition in list.files() when other
processes are operating on the directory has been fixed; the code
now dynamically allocates memory for file listings in a single
pass instead of making an initial count pass.

parse(text=x) misbehaved for objects x that
were not coerced internally to character, notably symbols.
(Reported to R-devel by Bill Dunlap.)

The internal C function coerceSymbol now handles
coercion to character, and warns if coercion fails (rather than
silently returning NULL). This allows a name to be given
where a character vector is required in functions which coerce
internally.

The interpretation by strptime() of "%c" was
non-standard (not that it is ever advisable to use locale- and
system-specific input formats).

capabilities("X11") now works the same way on Mac OS X as on
other platforms (and as documented: it was always true for R
built with --with-aqua, as the CRAN builds are).

The X11() device with cairo but not Pango (notably Mac OS X)
now checks validity of text strings in UTF-8 locales (since
Pango does but cairo it seems does not).

all.equal(tolerance = e) passes the numeric
tolerance also to the comparison of the attributes.

pgamma(0, 0), a boundary case, now returns 0, its
limit from the left, rather than the limit from the right.

Issuing POST requests to the internal web server could stall
the request under certain circumstances.

gzcon( <textConnection> ), an error, no longer
damages the connection (in a way to have it
segfault). (PR#14237)

All the results from hist() now use the nominal
breaks not those adjusted by the numeric ‘fuzz’:
in recent versions the nominal breaks were reported but
the 'density' referred to the intervals used in the calculation
– which mattered very slightly for one of the extreme bins.
(Based on a report by Martin Becker.)

If xy[z].coords (used internally by many graphics
functions) are given a list as x, they now check that
the list has suitable names and give a more informative error
message. (PR#13936)

CHANGES IN R VERSION 2.10.1 patched

NEW FEATURES

The handling of line textures in the postscript() and
pdf() devices was set up for round end caps (the only type
which existed at the time): it has now been adjusted for butt
endcaps.

lchoose(a, k) is now defined as
log(abs(choose(a,k))), analogously to lfactorial().

Although \eqn{} in Rd files is defined as a
‘verbatim’ macro, many packages expected \dots and
\ldots to be interpreted there (as was the case in R <
2.10.0), so this is now done (using an ellipsis in HTML
rendering).

Escaping of braces in quoted strings in R-code sections of
Rd files is allowed again. This had been changed for the new Rd
format in R 2.10.0 but was only documented on the developer site
and was handled inconsistently by the converters: text and
example conversion removed the escapes but HTML conversion did
not.

The PCRE library has been updated to version 8.01, a bug-fix
release.

tools::readNEWS() now accepts a digit as the first
character of a news section.

BUG FIXES

Using read.table(header=TRUE) on a header with an
embedded new line would copy part of the header into the data.
(PR#14103)

Changing both line texture and line cap (end) resulted in the
latter to be ommitted form the PDF code. In addition, line cap
(end) and join are now set explicitly in PDF output to ensure
correct defaults.

The suppression of auto-rotation in bitmap() and
dev2bitmap() with the "pdfwrite" device was not
working correctly.

plot(ecdf(), log="x") no longer gives an incorrect
warning.

read.fwf() works again when argument file is
a connection.

Startup files will now be found if their paths exceed 255
bytes. (PR#14228)

contrasts<- (in the stats package) no longer has an
undeclared dependence on methods (introduced in 2.10.0).

CHANGES IN R VERSION 2.10.1

NEW FEATURES

The PCRE library has been updated to version 8.00.

R CMD INSTALL has new options --no-R,
--no-libs, --no-data, --no-help,
--no-demo, --no-exec, and --no-inst to
suppress installation of the specified part of the package.
These are intended for special purposes (e.g. building a database
of help pages without fully installing all packages).

The documented line-length limit of 4095 bytes when reading
from the console now also applies also to parse(file="")
(which previously had a limit of around 1024 bytes).

A Bioconductor mirror can be set for use by
setRepositories()via the option "BioC_mirror",
e.g. the European mirror can be selected by
options(BioC_mirror="http://bioconductor.statistik.tu-dortmund.de").

Double-clicking in a tk_select.list() list box now
selects the item and closes the list box (as happens on the
Windows select.list() widget).

INSTALLATION

configure will be able to find a usable
libtiff in some rare circumstances where it did not
previously (where libtiff needed to be linked explicitly against
-ljpeg).

Making refman.pdf works around a problem with the indexing
with hyperref 6.79d and later.

DEPRECATED & DEFUNCT

The extended argument is deprecated in
strsplit(), grep(), grepl(), sub(),
gsub(), regexpr() and gregexpr() (not just
the value extended = FALSE) and will be removed in R
2.11.0.

BUG FIXES

trigamma(x) and other psigamma(x, n) calls
are now accurate for very large abs(x). (PR#14020)

[g]sub(perl=FALSE, fixed=FALSE) could use excessive
stack space when used with a very long vector containing some
non-ASCII strings.

The default method of weighted.mean(na.rm = TRUE)
did not omit weights for NA observations in 2.10.0.
(PR#14032)

[g]regexpr(pattern, fixed = TRUE) returned match
positions in bytes (not characters) in an MBCS locale if
pattern was a single byte.

[g]sub(fixed = TRUE) with a single-byte pattern could
conceivably have matched part of a multibyte character in a
non-UTF-8 MBCS.

findLineNum() and setBreakpoint() would
sometimes fail if the specified file was not in the current
directory.

Package tcltk's demo(tkdensity) was broken in
2.9.0 when demo() was changed to set par(ask = TRUE).

gsub() with backrefs could fail on extremely long strings
(hundreds of thousands of characters) due to integer overflow
in a length calculation.

detach()/unloadNamespace() arrange to flush
the package's lazyload cache of R objects once the
package/namespace is no longer needed.

There have been small fixes to the rendering of help,
e.g. \command is now rendered verbatim (so e.g. --
is not interpreted, PR#14045).

Also, there are many small changes to help files where the new
converters were not rendering them in the same way as before.

available.packages() would fail when run on a
repository with no packages meeting the filtering conditions.
(PR#14042)

rep(x, times, each = 2) gave invalid results when the
times argument was a vector longer than x.
Reported by Bill Dunlap.

An error when unloadNamespace() attempted to run the
.onUnload() function gave an error in the reporting
function and so was not reported properly.

Text help rendering did not handle very long input lines
properly.

promptMethods() generated signature documentation
improperly.

pgamma(x, a, lower.tail=FALSE) and
qgamma(...) are now considerably more accurate in some
regions for very small a. qgamma() now correctly
returns 0 instead of NaN in similar extreme cases,
and qgamma() no longer warns in the case of small
a, see (PR#12324).

It could return nonsensical results if no input determined the
number of cases (seen in the no-segfault tests).

An error in nls() with a long formula could cause a
segfault. (PR#14059)

qchisq(p, df, ncp, lower.tail = FALSE) with
ncp >= 80 was inaccurate for small p (as the help page
said): it is now less inaccurate. (In part,
PR#13999.)

For ncp less than but close to 80, pchisq() and
qchisq() are more accurate for probablilities very close
to 1 (a series expansion was truncated slightly too early).

pchisq(x, df, ncp) can no longer return values just larger
than one for large values of ncp.

intToUtf8() could fail when asked to produce 10Mb or more
strings, something it was never intended to do: unfortunately
Windows crashed R (other OSes reported a lack of resources).
(PR#14068)

chisq.test() could fail when given argument
x or y which deparsed to more than one line.
(Reported by Laurent Gauthier.)

S4 methods are uncached whenever the name space containing
them is unloaded (by unloadNamespace() as well as by
detach(unload = TRUE)).

The internal record-keeping by
dyn.load/dyn.unload was incomplete, which could
crash R if a DLL that registered .External routines had
earlier been unloaded.

bessel[JY](x, nu) with nu a negative integer (a
singular case) is now correct, analogously to besselI(),
see PR#13556.

tools::file_path_as_absolute() doubled the file
separator when applied to a file such as ‘"/vmunix"’ or (on
Windows) ‘"d:/afile"’ in a directory for which
getwd() would return a path with a trailing separator
(largely cosmetic, as reasonable file systems handle such a path
correctly). (Perhaps what was meant by PR#14078.)

unsplit(drop = TRUE) applied to a data frame failed
to pass drop to the computation of row names. (PR#14084)

The "difftime" method of mean() ignored its
na.rm argument.

tcltk::tk_select.list() is now more likely to remove the
widget immediately after selection is complete.

Adding/subtracting a "difftime" object to/from a
"POSIXt" or "Date" object works again (it was
broken by the addition of Ops.difftime).

Conversion to latex of an Rd file with no aliases failed.

wilcox.test(conf.int=TRUE) has achieved.level
corrected and, for exact=FALSE, now returns a
estimate component which does not depend on the
alternative used.

help.search() failed when the package argument was
specified. (PR#14113)

switch(EXPR = "A") now returns NULL, as does
switch(1) (which used to signal an error).

CHANGES IN R VERSION 2.10.0

SIGNIFICANT USER-VISIBLE CHANGES

Package help is now converted from Rd by the R-based
converters that were first introduced in 2.9.0. This means

Packages that were installed by R-devel after 2009-08-09
should not be used with earlier versions of R, and most
aspects of package help (including the runnable examples)
will be missing if they are so used.

Text, HTML and latex help and examples for packages
installed under the new system are converted on-demand from
stored parsed Rd files. (Conversions stored in packages
installed under R < 2.10.0 are used if no parsed Rd files
are found. It is recommended that such packages be
re-installed.)

HTML help is now generated dynamically using an HTTP server
running in the R process and listening on the loopback
interface.

Those worried about security implications of such
a server can disable it by setting the environment variable
R_DISABLE_HTTPD to a non-empty value. This disables
help.start() and HTML help (so text help is shown
instead).

The Java/Javascript search engine has been replaced by an
HTML interface to help.search(). help.start() no
longer has an argument searchEngine as it is no longer
needed.

The HTML help can now locate cross-references of the form
\link[pkg]{foo} and \link[pkg:foo]{bar}
where foo is an alias in the package, rather than the
documented (basename of a) filename (since the documentation
has been much ignored).

NEW FEATURES

polygon(), pdf() and postscript() now
have an argument fillOddEven (default FALSE),
which controls the mode used for polygon fills of
self-intersecting shapes.

New debugonce() function; further,
getOption("deparse.max.lines") is now observed when
debugging, from a code suggestion by John Brzustowski.
(PR#13647/8)

[g]sub(perl=TRUE) now also supports "\E"
in order to end"\U" and "\L" case changes,
thanks to a patch from Bill Dunlap.

factor(), `levels<-`(), etc, now ensure that
the resulting factor levels are unique (as was always the implied
intention). Factors with duplicated levels are still
constructible by low-level means, but are now declared illegal.

New print() (S3) method for class "function",
also used for auto-printing. Further, .Primitive
functions now print and auto-print identically. The new method
is based on code suggestions by Romain François.

The print() and toLatex() methods for class
"sessionInfo" now show the locale in a nicer format and
have arguments to suppress locale information.

In addition to previously only round(), there are
other Math group (S3) methods for "difftime",
such as floor(), signif(), abs(), etc.

For completeness, old.packages() and
available.packages() allow arguments type to be
specified (you could always specify arguments available
or contriburl).

available.packages() by default only returns
information on the latest versions of packages whose version
requirements are satisified by the currently running R.

tools::write_PACKAGES() has a new argument
latestOnly, which defaults to TRUE when only the
latest versions in the repository will be listed in the index.

getOption() has a new argument default that
is returned if the specified option is not set. This simplifies
querying a value and checking whether it is NULL or not.

parse() now warns if the requested encoding is not supported.

The "table" method of as.data.frame() gains a
stringsAsFactors argument to allow the classifying
factors to be returned as character vectors rather than the
default factor type.

If model.frame.default() encounters a character
variable where xlev indicates a factor, it now converts
the variable to a factor (with a warning).

curve() now returns a list containing the points that
w§ere drawn.

spineplot() now accepts axes = FALSE, for
consistency with other functions called by plot.factor().

The Kendall and Spearman methods of cor.test() can
optionally use continuity correction when not computing exact
p-values. (The Kendall case is the wish of PR#13691.)

R now keeps track of line numbers during execution for code
sourced with options(keep.source = TRUE). The source
reference is displayed by debugging functions such as
traceback(), browser(), recover(), and
dump.frames(), and is stored as an attribute on each
element returned by sys.calls().

More functions now have an implicit (S4) generic definition.

quantile.default() now disallows factors (wish of
PR#13631) and its help
documents what numeric-like properties its input need to have to
work correctly.

weighted.mean() is now generic and has "Date",
"POSIXct" and "POSIXlt" methods.

Naming subscripts (e.g. x[i=1, j=2]) in
data.frame methods for [ and [[ now gives a
warning. (Names are ignored in the default method, but could
have odd semantics for other methods, and do for the data.frame
ones.)

as.character(x) for numeric x no longer
produces strings such as "0.30", i.e., with trailing
zeros. This change also renders levels construction in
factor() more consistent.

codocClasses(), which checks consistency of the
documentation of S4 class slots, now does so in considerably more
cases. The documentation of inherited slots (from superclasses)
is now optional. This affects R CMD check <pkg> when
the package defines S4 classes.

codoc() now also checks S4 methods for code/documentation
mismatches.

for(), while(), and repeat() loops now
always return NULL as their (invisible) value. This change was
needed to address a reference counting bug without creating
performance penalties for some common use cases.

The print() method for ls.str() results now
obeys an optional digits argument.

The method argument of glm() now allows
user-contributed methods.

More general reorder.default() replaces functionality of
reorder.factor() and reorder.character().

The function aspell() has been added to provide an
interface to the Aspell spell-checker.

Filters RdTextFilter() and SweaveTeXFilter()
have been added to the tools package to provide support for
aspell() or other spell checkers.

xtabs() with the new argument sparse = TRUE
now returns a sparse Matrix, using package Matrix.

contr.sum() etc gain an argument sparse
which allows sparse matrices to be returned.

contrasts() also gains a sparse argument which it
passes to the actual contrast function if that has a formal
argument sparse.

contrasts(f, .) <- val now also works when val
is a sparse Matrix. It is planned that model.matrix()
will work with such factors f in the future.

readNEWS() will recognize a UTF-8 byte-order mark
(BOM) in the ‘NEWS’ file. However, it is safer to use only
ASCII code there because not all editors recognize BOMs.

New utility function inheritedSlotNames() for S4
class programming.

tabulate() now allows NAs to pass through (and be ignored).

If debug() is called on an S3 generic function then
all methods are debugged as well.

svd(x) and eigen(x) now behave analogously to
qr(x) in accepting logical matrices x.

File ‘NEWS’ is now in UTF-8, and has a BOM (often
invisible) on the first line, and Emacs local variables
set for UTF-8 at the end. RShowDoc("NEWS") should display
this correctly, given suitable fonts.

terms.formula(simplify = TRUE) now does not deparse
the LHS and so preserves non-standard responses such as `a:
b` (requested by Sundar Dorai-Raj).

New function news() for building and querying R or
package news information.

z^n for integer n and complex z is more
accurate now if |n| <= 65536.

factor(NULL) now returns the same as
factor(character(0)) instead of an error, and
table(NULL) consequently does analogously.

as.data.frame.vector() (and its copies) is slightly faster
by avoiding a copy if there are no names (following a
suggestion of Tim Hesterberg).

writeLines(), writeBin() and
writeChar() have a new argument useBytes. If
false, character strings with marked encodings are translated to
the current locale (as before) but if true they are written
byte-by-byte.

iconv() has a new argument mark which can be
used (by experts) to suppress the declaration of encodings.

‘DESCRIPTION’ file's LinkingTo specs are now
recognized as installation dependencies, and included in package
management computations.

Standardized ‘DESCRIPTION’ file License specs
are now available for package management computations.

"\uxxxx" and "\Uxxxxxxxx" escapes can now be
parsed to a UTF-8 encoded string even in non-UTF-8 locales (this
has been implemented on Windows since R 2.7.0). The semantics
have been changed slightly: a string containing such escapes is
always stored in UTF-8 (and hence is suitable for portably
including Unicode text in packages).

Rd.sty now makes a better job of setting email addresses,
including using a monospaced font.

textConnection() gains an encoding argument
to determine how input strings with marked encodings will be
handled.

R CMD Rd2pdf is available as a shortcut for
R CMD Rd2dvi --pdf.

R CMD check now checks links where a package is
specified (\link[pkg]{file} or
\link[pkg:file]{topic}), if the package is available.
It notes if the package is not available, as in many cases this
is an error in the link.

identical() gains three logical arguments, which
allow for even more differentiation, notably -0 and
0.

legend() now can specify the border color of
filled boxes, thanks to a patch from Frederic Schutz.

Indexing with a vector index to [[ ]] has now been
extended to all recursive types.

Pairlists may now be assigned as elements of lists. (Lists
could always be created with pairlist elements, but [[<-
didn't support assigning them.)

The parser now supports C-preprocessor-like #line
directives, so error messages and source references may refer to
the original file rather than an intermediate one.

New functions findLineNum() and
setBreakpoint() work with the source references to find
the location of source lines and set breakpoints (using
trace()) at those lines.

Namespace importing is more careful about warning on masked
generics, thanks to a patch by Yohan Chalabi.

detach() now has an argument character.only
with the same meaning as for library() or
require().

available.packages() gains a filters
argument for specifying the filtering operations performed on the
packages found in the repositories. A new built-in
"license/FOSS" filter only retains packages for which
installation can proceed solely based on packages which can be
verified as Free or Open Source Software (FOSS) employing the
available license specifications.

In registering an S3 class by a call to
setOldClass(), the data part (e.g., the object type)
required for the class can be included as one of the superclasses
in the Classes argument.

The argument f to showMethods() can be an
expression evaluating to a generic function, allowing methods to
be shown for non-exported generics and other nonstandard cases.

sprintf() now supports %o for octal
conversions.

New function Sys.readlink() for information about symbolic
links, including if a file is a symbolic link.

Package tools has new functions
checkRdaFiles() and resaveRdaFiles() to report on
the format of ‘.rda’/‘.RData’ data files, and to
re-save them in a different compressed format, including choosing
the most compact format available.

A new INSTALL option, --resave-data, makes use
of this.

File ‘~/.R/config’ is used in preference to
‘~/.Rconfig’, and these are now documented in ‘R
Installation and Administration’.

Logic operations with complex numbers now work, as they were always
documented to, and as in S.

arrows() and segments() allow one of x1
or y1 to be omitted to simplify the specification of
vertical or horizontal lines (suggestion of Tim Hesterberg).

There are the beginnings of a Nynorsk translation by Karl Ove
Hufthammer.

stripchart() allows parbg to be
passed in for the background colour for pch = 21 (wish of
PR#13984).

New generic function .DollarNames() to enable class authors
to customize completion after the $ extractor.

load(), save(), dput() and
dump() now open a not-yet-open connection in the
appropriate mode (as other functions using connections directly
already did).

REGULAR EXPRESSIONS

A different regular expression engine is used for basic and
extended regexps and is also for approximate matching. This is
based on the TRE library of Ville Laurikari, a modifed copy of
which is included in the R sources.

This is often faster, especially in a MBCS locale.

Some known differences are that it is less tolerant of invalid
inputs in MBCS locales, and in its interpretation of undefined
(extended) regexps such as "^*". Also, the interpretation of
ranges such as [W-z] in caseless matching is no longer to map
the range to lower case.

This engine may in future be used in ‘literal’ mode for
fixed = TRUE, and there is a compile-time option in
src/main/grep.c to do so.

The use of repeated boundary regexps in gsub() and
gregexpr() as warned about in the help page does not work
in this engine (it did in the previous one since 2005).

Extended (and basic) regexps now support same set of options
as for fixed = TRUE and perl = TRUE, including
useBytes and support for UTF-8-encoded strings in
non-UTF-8 locales.

agrep() now has full support for MBCS locales with a modest
speed penalty. This enables help.search() to use approximate
matching character-wise rather than byte-wise.

[g]sub use a single-pass algorithm instead of
matching twice and so is usually faster.

The perl = TRUE versions now work correctly in a
non-UTF-8 MBCS locale, by translating the inputs to UTF-8.

useBytes = TRUE now inhibits the translation of inputs with
marked encodings.

strsplit() gains a useBytes argument.

The algorithm used by strsplit() has been reordered
to batch by elements of split: this can be much faster for
fixed = FALSE (as multiple compilation of regexps is avoided).

The help pages, including ?regexp, have been updated
and should be consulted for details of the new implementations.

HELP & Rd FILE CHANGES

A new dynamic HTML help system is used by default, and may be
controlled using tools::startDynamicHelp(). With this enabled,
HTML help pages will be generated on request, resolving links
by searching through the current .libPaths(). The user
may set options("help.ports") to control which IP port is used
by the server.

help.start() no longer sets options(htmlhelp =
TRUE) (it used to on Unix but not on Windows). Nor does it on
Unix reset the "browser" option if given an argument of
that name.

Arguments update and remote are now available
on all platforms: the default is update = FALSE since the
http server will update the package index at first use.

help() has a new argument help_type (with
default set by the option of that name) to supersede arguments
offline, htmlhelp and chmhelp
(although for now they still work if help_type is
unset). There is a new type, "PDF" to allow offline PDF
(rather than PostScript).

A function offline_help_helper() will be used if this exists
in the workspace or further down the search path, otherwise
the function of that name in the utils name space is used.

Plain text help is now used as the fallback for HTML help (as
it always was for Compiled HTML help on Windows).

It is possible to ask for static HTML pages to be prebuilt
via the configure option --enable-prebuilt-html. This
may be useful for those who wish to make HTML help available
outside R, e.g. on a local web site.

An experimental tag \Sexpr has been added to Rd
files, to evaluate expressions at build, install, or render time.
Currently install time and render time evaluation are supported.

Tags \if, \ifelse and \out have been
added to allow format-specific (or more general, using
\Sexpr) conditional text in man pages.

The parse_Rd() parser has been made more tolerant of coding
errors in Rd files: now all syntax errors are reported as
warnings, and an attempt is made to continue parsing.

parse_Rd() now has an argument fragment
(default FALSE) to accept small fragments of Rd files (so
that \Sexpr can output Rd code which is then parsed).

parse_Rd() now always converts its input to UTF-8.
The Rd2* rendering functions have a new argument,
outputEncoding, which controls how their output is
encoded.

parse_Rd() no longer includes the newline as part of
a "%"-style comment.

There have been various bug fixes and code reorganization in
the Rd renderers Rd2HTML, Rd2latex, Rd2txt,
and Rd2ex.

All example files are now created with either ASCII or UTF-8
encoding, and the encoding is only marked in the file if there
is any non-UTF-8 code (previously it was marked if the help
file had non-ASCII contents, possibly in other sections).

print.Rd() now adds necessary escape characters so that
printing and re-parsing an Rd object should produce an
equivalent object.

parse_Rd() now recognizes the \var tag within
a quoted string in R-like text.

parse_Rd() now treats the argument of
\command as LaTeX-like, rather than verbatim.

COMPRESSION

New function untar() to list or unpack tar archives,
possibly compressed. This uses either an external tar
command or an internal implementation.

New function tar() to create (possibly compressed)
tar archives.

New functions memCompress() and
memDecompress() for in-memory compression and
decompression.

bzfile() has a compress argument to select
the amount of effort put into compression when writing.

New function xzfile() for use with
xz-compressed files. (This can also read files
compressed by some versions of lzma.)

gzfile() looks at the file header and so can now also
read bzip2-ed files and xz-compressed files.

There are the new options of save(compress = "bzip2")
and "xz" to use bzip2 or xz
compression (which will be slower, but can give substantially
smaller files). Argument compression_level gives finer
control over the space/time tradeoffs.

load() can read such saves (but only as from this version of R).

R CMD INSTALL/check and
tools::writePACKAGES accept a wider range of compressed
tar archives. Precisely how wide depends on the capabilities of
the host system's tar command: they almost always
include .tar.bz2 archives, and with modern versions of
tar other forms of compression such as lzma
and xz, and arbitrary extensions.

R CMD INSTALL has a new option
--data-compress to control the compression used when
lazy-loading data. New possibilities are
--data-compress=bzip2 which will give ca 15% better
compression at the expense of slower installation times, and
--data-compress=xz, often giving even better compression
on large datasets at the expense of much longer installation
times. (The latter is used for the recommended packages: it is
particularly effective for survival.)

file() for open = "", "r" or
"rt" will automagically detect compressed files (from
gzip, bzip2 or xz). This means
that compressed files can be specified by file name (rather than
via a gzfile() connection) to read.table(),
readlines(), scan() and so on.

DEPRECATED & DEFUNCT

tools::Rd_parse() is defunct (as this version of R
uses only Rd version 2).

Use of file ‘~/.Rconf’ (which was deprecated in favour
of ‘~/.Rconfig’ in 2004) has finally been removed.

Bundles of packages are deprecated. See ‘Writing R
Extensions’ for the steps needed to unbundle a bundle.

help() arguments offline, htmlhelp and
chmhelp are deprecated in favour of help_type.

clearNames() (in package stats) is deprecated
for unname().

Basic regular expressions (extended = FALSE) are
deprecated in strsplit, grep and friends. There is
a precise POSIX standard for them, but it is not what recent RE
engines implement, and it seems that in almost all cases package
authors intended fixed = TRUE when using extended =
FALSE.

methods::trySilent() is deprecated in favour of
try(silent=TRUE) or – more efficiently and flexibly –
something like tryCatch(error = function(e) e).

index.search() is deprecated: there are no longer
directories of types other than help.

INSTALLATION

cairo >= 1.2 is now required (1.2.0 was released in July 2006)
for cairo-based graphics devices (which remain optional).

A suitable iconv() is now required: support for
configure option --without-iconv has been withdrawn (it
was deprecated in R 2.5.0).

Perl is no longer ‘essential’. R can be built
without it, but scripts R CMD build, check,
Rprof and Sd2d currently require it.

A system glob function is now essential (a working
Sys.glob() has been assumed since R 2.9.0 at least).

C99 support for MBCS is now required, and configure option
--disable-mbcs has been withdrawn.

Having a version of tar capable of automagically
detecting compressed archives is useful for
utils::untar(), and so gtar (a common name for
GNU tar) is preferred to tar: set environment
variable TAR to specify a particular tar command.

INTERNATIONALIZATION

There is some makefile support for adding/updating translations
in packages: see po/README and ‘Writing R Extensions’.

There is support for the use of dngettext for C-level
translations in packages: see ‘Writing R Extensions’.

BUG FIXES

Assigning an extra 0-length column to a data frame by
DF[, "foo"] <- value now works in most cases (by filling
with NAs) or fails. (It used to give a corrupt data
frame.)

validObject() avoids an error during evaluation in the case
of various incorrect slot definitions.

n:m now returns a result of type "integer" in
a few more boundary cases.

The zap.ind argument to printCoefmat() did
not usually work as other code attempted to ensure that non-zero
values had a non-zero representation.

printCoefmat() formatted groups of columns together,
not just the cs.ind group but also the zap.ind
group and a residual group. It now formats all columns except
the cs.ind group separately (and zaps the zap.ind
group column-by-column). The main effect will be see in the
output from print.anova(), as this grouped SS-like columns
in the zap.ind group.

R_ReplDLLinit() initializes the top-level jump so
that some embedded applications on Windows no longer crash on
error.

identical() failed to take the encoding of character
strings into account, so identical byte patterns are not
necessarily identical strings, and similarly Latin-1 and UTF-8
versions of the same string differ in byte pattern.

methods(f) used to warn unnecessarily for an S4
generic f which had been created based on an existing S3
generic.

The check for consistent ordering of superclasses was not
ignoring all conditional relations (the symptom was usually
spurious warnings for classes extending "array").

Trying to assign into a raw vector with an index vector
containing NAs could cause a segfault. Reported by Hervé
Pagès.

Rscript could segfault if (by user error) its
filename argument was missing. Reported by Martin Morgan.

getAnywhere() (and functions that use it, including argument
completion in the console) did not handle special built-in
functions. Reported by Romain Francois.

order() was missing a PROTECT() call and so
could segfault when called on character data under certain (rare)
circumstances involving marked non-native encodings.

prettyNum(z, drop0trailing=TRUE) did not work
correctly when z was a complex vector. Consequently,
str(z, ...) also did not. (PR#13985)

make distclean removed too many files in
etc/ if builddir = srcdir.

R CMD replaced TEXINPUTS rather than
appending to it (as documented and intended).

help.start() no longer fails on unix when
"browser" is a function.

pbeta(x, ..., log.p = TRUE) is sometimes more accurate,
e.g., for very small x.

Unserializing a pre-2.8 workspace containing pure ASCII
character objects with a Latin-1 or UTF-8 encoding would corrupt
the CHARSXP cache.